During our distance calculation we make two assumptions.
1) We assume a spherical Earth as a close approximation of the true shape of the Earth (an oblate spheroid). The distance is calculated as great-circle or orthodromic distance on the surface of a sphere.
2) We choose a particular point inside each city as the "city centre" and calculate the distances using coordinates of these "city centres". Real distances between other points inside or near these cities will slightly differ.